MiMeDB: Showing metabocard for alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate (MMDBc0031928)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:55:20 UTC

Update Date

2022-08-31 18:26:31 UTC

Metabolite ID

MMDBc0031928

Metabolite Identification

Common Name

alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate

Description

A ribose bisphosphate that is the cyclic-1,2-phosphate derivative of 5-phospho-Œ±-D-ribose

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041521132D          
 
 17 18  0  0  1  0            999 V2000
   13.5056   -9.3121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8653   -9.6426    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.1874   -9.1349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6082  -10.3866    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.5267   -9.6078    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.7840  -10.3866    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.7409   -9.3540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1255   -9.9103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2911   -9.9103    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.4601   -9.9103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2876  -10.7413    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2876   -9.0792    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.6546  -11.2241    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.0781  -10.3021    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   14.9099   -9.7221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3361  -10.9747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3031  -11.0517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
  5  6  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
  1 14  1  0  0  0  0
  4 16  1  6  0  0  0
  6 17  1  6  0  0  0
 16 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031928

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@@H]1[C@@H](COP(O)(O)=O)O[C@@H]2OP(O)(=O)O[C@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O10P2/c6-3-2(1-12-16(7,8)9)13-5-4(3)14-17(10,11)15-5/h2-6H,1H2,(H,10,11)(H2,7,8,9)/t2-,3-,4-,5-/m1/s1

> <INCHI_KEY>
OXGUIUWFXGIWNM-TXICZTDVSA-N

> <FORMULA>
C5H10O10P2

> <MOLECULAR_WEIGHT>
292.073

> <EXACT_MASS>
291.974920518

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
21.278615144831434

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(3aR,5R,6R,6aR)-2,6-dihydroxy-2-oxo-tetrahydro-2H-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-1.16

> <JCHEM_LOGP>
-1.6527985473333333

> <ALOGPS_LOGS>
-1.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
1.691496559433233

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0421745627044876

> <JCHEM_PKA_STRONGEST_BASIC>
-3.702127883947399

> <JCHEM_POLAR_SURFACE_AREA>
151.98

> <JCHEM_REFRACTIVITY>
47.9277

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.06e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3aR,5R,6R,6aR)-2,6-dihydroxy-2-oxo-tetrahydro-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  O   UNK     0      25.210 -17.383   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      24.015 -18.000   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      22.750 -17.052   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      23.535 -19.388   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      21.517 -17.935   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      21.997 -19.388   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      20.050 -17.461   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      18.901 -18.499   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0      17.343 -18.499   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0      15.792 -18.499   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      17.337 -20.050   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      17.337 -16.948   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      27.355 -20.952   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0      26.279 -19.231   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0      27.832 -18.148   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      24.894 -20.486   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      21.099 -20.630   0.000  0.00  0.00           O+0
CONECT    1    2   14                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2    5                                                       
CONECT    4    2    6   16                                                  
CONECT    5    3    7    6                                                  
CONECT    6    4    5   17                                                  
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13   14                                                            
CONECT   14   13   15    1   16                                             
CONECT   15   14                                                            
CONECT   16    4   14                                                       
CONECT   17    6                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

Synonyms

Value	Source
5-O-Phosphono-alpha-D-ribofuranose 1,2-(hydrogen phosphate)	ChEBI
PRCP	ChEBI
5-Phospho-alpha-D-ribose 1,2-cyclic phosphate	Kegg
5-O-Phosphono-a-D-ribofuranose 1,2-(hydrogen phosphate)	Generator
5-O-Phosphono-a-D-ribofuranose 1,2-(hydrogen phosphoric acid)	Generator
5-O-Phosphono-alpha-D-ribofuranose 1,2-(hydrogen phosphoric acid)	Generator
5-O-Phosphono-α-D-ribofuranose 1,2-(hydrogen phosphate)	Generator
5-O-Phosphono-α-D-ribofuranose 1,2-(hydrogen phosphoric acid)	Generator
5-Phospho-a-D-ribose 1,2-cyclic phosphate	Generator
5-Phospho-a-D-ribose 1,2-cyclic phosphoric acid	Generator
5-Phospho-alpha-D-ribose 1,2-cyclic phosphoric acid	Generator
5-Phospho-α-D-ribose 1,2-cyclic phosphate	Generator
5-Phospho-α-D-ribose 1,2-cyclic phosphoric acid	Generator
a-D-Ribose 1,2-cyclic phosphate 5-phosphate	Generator
a-D-Ribose 1,2-cyclic phosphoric acid 5-phosphoric acid	Generator
alpha-D-Ribose 1,2-cyclic phosphoric acid 5-phosphoric acid	Generator
Α-D-ribose 1,2-cyclic phosphate 5-phosphate	Generator
Α-D-ribose 1,2-cyclic phosphoric acid 5-phosphoric acid	Generator

Molecular Formula

C₅H₁₀O₁₀P₂

Average Mass

292.073

Monoisotopic Mass

291.974920518

IUPAC Name

{[(3aR,5R,6R,6aR)-2,6-dihydroxy-2-oxo-tetrahydro-2H-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxy}phosphonic acid

Traditional Name

[(3aR,5R,6R,6aR)-2,6-dihydroxy-2-oxo-tetrahydro-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@@H](COP(O)(O)=O)O[C@@H]2OP(O)(=O)O[C@H]12

InChI Identifier

InChI=1S/C5H10O10P2/c6-3-2(1-12-16(7,8)9)13-5-4(3)14-17(10,11)15-5/h2-6H,1H2,(H,10,11)(H2,7,8,9)/t2-,3-,4-,5-/m1/s1

InChI Key

OXGUIUWFXGIWNM-TXICZTDVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Monosaccharide phosphate
Monoalkyl phosphate
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
1,3_dioxaphospholane
Tetrahydrofuran
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Hydrocarbon derivative
Organic oxide
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

ribose bisphosphate (CHEBI:68689 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	20.6 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-1.7	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	1.04	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	151.98 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	47.93 m³·mol⁻¹	ChemAxon
Polarizability	21.28 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0007-1690000000-d822c489f37b24ff2975	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-6950000000-ffcb5885e5ecb4a2905a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0005-9400000000-03837736df41b9fe2d72	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002f-6190000000-409357fcff55c5c65e9e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9010000000-43b002ba2f4ac1d81b59	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-f05162e8bfcafc437f6e	2015-09-15	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0015378	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate	Ribose 1,5-bisphosphate	Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	RHEA	34755880
MMDBr0015807	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate	D-ribose 2,5-bisphosphate	Phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	RHEA	34755880
MMDBr0019291	alpha-D-Ribose 1-methylphosphonate 5-phosphate	Methane	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase	Non-hydrolytic bond cleavage (or its reversal)	PathBank	31602464
MMDBr0019292	Water	Hydrogen Ion	Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	PathBank	31602464
MMDBr0024932	S-Adenosylmethionine	Hydrogen Ion	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase	Non-hydrolytic bond cleavage (or its reversal)	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria	Actinobacteria	1	Human ; Human feces

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C20440

BioCyc ID

CPD0-2463

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14035690

PDB ID

Not Available

ChEBI ID

68689

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate (MMDBc0031928)

MOL for #<Metabolite:0x00007fa4900f09d8>

3D MOL for #<Metabolite:0x00007fa4900f09d8>

3D SDF for #<Metabolite:0x00007fa4900f09d8>

3D-SDF for #<Metabolite:0x00007fa4900f09d8>

PDB for #<Metabolite:0x00007fa4900f09d8>

3D PDB for #<Metabolite:0x00007fa4900f09d8>

SMILES for #<Metabolite:0x00007fa4900f09d8>

INCHI for #<Metabolite:0x00007fa4900f09d8>

Structure for #<Metabolite:0x00007fa4900f09d8>

3D Structure for #<Metabolite:0x00007fa4900f09d8>